Antimalarial drugs impose strong pressure on Plasmodium falciparum parasites and leave signatures of selection in the parasite genome 1,2. Search for signals of selection may lead to genes encoding drug or immune targets 3. The lack of high-throughput genotyping methods, inadequate knowledge of parasite population history, and time-consuming adaptations of parasites to in vitro culture have hampered genome-wide association studies (GWAS) of parasite traits. Here we report genotyping of DNA from 189 culture-adapted P. falciparum parasites using a custom-built array with thousands of single nucleotide polymorphisms (SNPs). Population structure, variation in recombination rate, and loci under recent positive selection were detected. Parasite half maximum inhibitory concentrations (IC50) to seven antimalarial drugs were obtained and used in GWAS to identify genes associated with drug responses. The SNP array and genome-wide parameters provide valuable tools and information for new advances in P. falciparum genetics.

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Plasmodium yoelii is an excellent model for studying malaria pathogenesis that is often intractable to investigate using human parasites; however, genetic studies of the parasite have been hindered by lack of genome-wide linkage resources. Here, we performed 14 genetic crosses between three pairs of P. yoelii clones/subspecies, isolated 75 independent recombinant progeny from the crosses, and constructed a high-resolution linkage map for this parasite. Microsatellite genotypes from the progeny formed 14 linkage groups belonging to the 14 parasite chromosomes, allowing assignment of sequence contigs to chromosomes. Growth-related virulent phenotypes from 25 progeny of one of the crosses were significantly associated with a major locus on chromosome 13 and with two secondary loci on chromosomes 7 and 10. The chromosome 10 and 13 loci are both linked to day 5 parasitemia, and their effects on parasite growth rate are independent but additive. The locus on chromosome 7 is associated with day 10 parasitemia. The chromosome 13 locus spans ∼220 kb of DNA containing 51 predicted genes, including the P. yoelii erythrocyte binding ligand, in which a C741Y substitution in the R6 domain is implicated in the change of growth rate. Similarly, the chromosome 10 locus spans ∼234 kb with 71 candidate genes, containing a member of the 235-kDa rhoptry proteins (Py235) that can bind to the erythrocyte surface membrane. Atypical virulent phenotypes among the progeny were also observed. This study provides critical tools and information for genetic investigations of virulence and biology of P. yoelii.genetic mapping | inheritance | crossover | rodent

Intraplate volcanism initiated shortly after the cessation of Cenozoic seafloor spreading in the South China Sea (SCS) region, but the full extent of its influence on the Indochina block has not been well constrained. Here we present major and trace element data and Sr-Nd-Pb-Hf isotope ratios of late Cenozoic basaltic lavas from the Khorat plateau and some volcanic centers in the Paleozoic Sukhothai arc terrane in Thailand. These volcanic rocks are mainly trachybasalts and basaltic trachyandesites. Trace element patterns and Sr-Nd-Pb-Hf isotopic compositions show that these alkaline volcanic lavas exhibit oceanic island basalt (OIB)-like characteristics with enrichments in both large-ion lithophile elements (LILE) and high field strength elements (HFSEs). Their mantle source is a mixture between a depleted Indian MORB-type mantle and an enriched mantle type 2 (EMII). We suggest that the post-spreading intraplate volcanism in the SCS region was induced by a Hainan mantle plume which spread westwards to the Paleozoic Sukhothai arc terrane.

Sediments from the continental shelf are sensitive to sea level, climatic changes, and local tectonic history. In this study, we carried out a high-resolution magnetostratigraphic investigation on the longest core (NHH01, 125.64 m) recovered from the South Yellow Sea (SYS). An abnormal interval dominated by negative inclinations was discovered by applying alternating field demagnetization (AFD) on samples from a greigite-bearing layer (44.90-51.80 m). In contrast, the inclinations of most greigite-bearing samples changed from negative to positive when heated to~360°C. This strongly indicates that this inclination anomaly revealed by the AFD alone is not a true negative subchron. After neglecting the effects of greigite-bearing layers, the straightforward correlation of the interpreted magnetostratigraphy defines the Matuyama-Brunhes boundary (781 ka) and the Jaramillo top (990 ka) at 68.64 m and 101.54 m, respectively. The linearly extrapolated basal age of the core is~1.10 Ma. In addition, several short-lived inclination anomalies can be tentatively assigned to magnetic excursions, which indicates that the sedimentation could be continuous even at the millennial time scale at depth intervals bracketing these fast geomagnetic events. Moreover, the excellent correspondence between clay content variations of the core and the marine oxygen isotope record indicates the potential of clay content as a paleoclimatic proxy in the studied region in the past~1 Ma. In brief, our study provides not only a robust age model in the SYS but also a methodological guide for paleomagnetic studies in continental shelf region.

Studying drug resistance in Plasmodium falciparum requires accurate measurement of parasite response to a drug. Factors such as mixed infection of drug-resistant and -sensitive parasites can influence drug test outcome. Polymorphic DNA sequences are frequently used to detect mixed infections; infections with a single genotype or having a minor allele smaller than a subjectively selected cut-off value are often considered single infection. We studied the effects of mixed parasite populations containing various ratios of parasites resistant and sensitive to chloroquine on outcomes of drug tests and how ratios of parasite mixtures correlated with genotypes using polymerase chain reaction-based methods. Our results show that a mixture with a resistant population as low as 10% could greatly impact a drug test outcome. None of the genotyping methods could reliably detect minor DNA alleles at < or = 10%. Mixed infection presents a serious problem for drug tests, and genotyping using microsatellite or other methods may not reliably reflect true ratios of alleles.

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